The Legend of Zelda: Equestrian Shadows
by Ironman64
Summary: After saving the people of Termina in Majora's Mask, Link and Epona are pulled into a dark Equestria where King Sombra was able to take control. After coming across a local resistance, Link decides to help free this new world, by finding the Elements of Harmony and defeating Sombra just like he did Ganondorf. (Borrows plot details and elements from the games and the manga's)
1. Prologue

Disclaimer- I own none these properties involved in this crossover

My Little Pony is owned by Hasbro

The Legend of Zelda is owned by Nintendo

Constructive criticism is welcome and encouraged

* * *

**The Crystal Empire, Ten Years Ago...**

* * *

"You have to be the one to bring the Crystal Heart to the Faire" Twilight said to her dragon assistant through the dark crystal cage that she was trapped in.

"Me?" Spike said in shock at the unicorns request, he then took a look at the several black crystals that where approaching him. "But Twilight-" the dragon began to protest before Twilight cut him off.

"Go."

"-But-"

"GOOOOOOOOO!" Twilight finally shouted earning a look of panic from Spike, the dragon then scooped up the Crystal Heart in his sweaty palms and then jumped straight out of the window. As Spike went to deliver the heart, Twilight was still trying to escape the dark crystal prison but all her attempts where in vain as the prision kept resisting all of the spells that she cast at it.

A few hours later, Twilight was overtaken by darkness and the menacing figure of King Sombra was seen towering over her with a dark grin on his face. "**So, you're the unicorn who has tried to halt the retaking of my kingdom**" the unicorn king said in a dark, menacing voice causing Twilights pupils to shrink.

"Wh-what do you mean by tried?" Twilight said with fear in his voice, as if to answer Sombra's horn lit up to lower the cage that had her trapped. When it was lowered Twilight was surrounded by her friends, her brother and her sister in-law, all of which had glowing green eyes "n-no" Twilight silently muttered as she heard King Sombra laughing evilly.

"**As you can see, your friends and family are firmly under my control**" Sombra said as he brought a hoof underneath Twilights chin to make eye contact with her "**my faithful student**" the king finished with a mocking voice.

"What are you talking about?" Twilight said as she glared at the dark unicorn.

"**You have potential Twilight Sparkle, but you should know that Celestia is holding you back**" the king of the Crystal Empire said in a more persuasive tone of voice. "**I saw how easy it was for you to use dark magic while you where searching for the Crystal Heart, but you still lack the necercary power to control it, with my help I can teach you things even Celestia couldn't**" Sombra offered as he extended a hoof to the beaten unicorn.

In response Twilight just slapped Sombras hoof away and shot him an anger filled glare "take your offer and shove it Sombra, I'll never join you!" Twilight shouted earning a sinister laugh from the Crystal King.

"**If thats the way you want it, then so be it**" Sombra said in a dark voice as he turned his attention to Twilights friends and family. "**Take her to the dungeon, I don't want her to interrupt my conquest of Equestria**" the dark unicorn ordered as they advanced on the lavender pony.**  
**

"Yes master" Twilights friends all droned as they began to advance on Twilight, who attempted to fight off the advancing ponies, but the various attempts to escape the cage from earlier had left her exhausted. The brainwashed ponies dragged Twilight all the way down to the dungeon and threw her into a cell, as Sombra just grinned menacingly before leaving to plot his takeover of Equestria.

Twilight just sat in the centre of the cell with a blank expression on her face and tears beginning to form in her eyes. "Please just let this be a horrible nightmare" the lavender unicorn said while she cried herself to sleep.

* * *

**Ironman64 presents:**

**The Legend of Zelda: Equestrian Shadows**

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**Meanwhile, in the Kingdom of Hyrule...**

* * *

Link and Epona emerged from the Lost Woods, it had been at least a week since the near apocalyptic events in Termina and the Hero of Time felt unfulfilled. While he was happy that he was able to help out the citizens of Clock Town, he only wished that he could've found his fairy partner Navi on his journey through the woods.

"I hope she's okay, I'm worried that something might've happened to her" Link said in a concerned tone of voice as he looked down at his horse, who was looking at her friend with worried look on her face. "Don't worry about me girl, lets just get you back to Lon Lon Ranch before Malon kills me" Link said giving the horse a small smile as they began their long journey across Hyrule Field.

However before they reached the ranch the young hylian noticed something coming from a nearby cave, a faint blue glow. "What in the name of Nayru?" Link said as he dismounted Epona and started to walk slowly over to the cave, unknown to him his horse began following behind him very slowly as if something was calling her to the cave.

"N-Navi, are you in here?" called the Hero of Time as he recalled the glow reminded him of lost friend, but to his disappointment when headed deeper into the cave Navi was nowhere to be seen. However, what he found was some strange hieroglyphics bathed in a blue light, said hieroglyphics included a star, three apples, three butterflies, three balloons, three diamonds and a cloud with a lightning bolt.

But that wasn't the strange part about all this, the strange part was that getting closer to the wall with the images on it caused the symbol of the Triforce of Courage that was on his hand to glow brightly. "What in Din's name is this place?" Link questioned to himself only to be snapped out of his thoughts when he noticed a covered up Triforce insignia on the ground in front of him, remembering what Impa taught him during his first quest Link pulled out his ocarina and began playing Zelda's Lullaby.

After the Hero of Time finished the song he waited to see what the effect would be, to his surprise the pictures on the wall started to glow various colours and began to form what seemed to bright doorway. Link started to back away from it but the young hylian felt some kind of suction pulling him towards it, he tried to run but within mere seconds Link was swept off his feet and pulled through the bright doorway.

Epona, who was watching the whole thing occur from far away just ran at the bright doorway and jumped right through it before it sealed up, leaving Link and Epona to their fate.

* * *

"Ugh, my head" Link groaned as he started to regain consciousness, as he awoke the Hylian Hero found himself in the middle of a forest, which he assumed was Kokiri Forest at the time. As he picked himself up, he decided to check his item pouch to see whether he'd lost anything, to his relief almost everything was still there, his bow and arrows, hookshot, boomerang, his various masks and all his bottles, which had all of their contents intact.

However the Hero of Time was missing something extremely important "where's my ocarina?" he asked himself as he searched all around the area that he had landed in, unfortunately his efforts where all in vain. "Not again" Link said in a pathetic voice as he wondered where the blue instrument was.

However he didn't get long to think about it as a loud scream brought him out of his stunned state "HELP! somebody please, HELP ME!" cried a young female voice which sounded close to his location. As if it was by instinct, Link followed the sound of the voice to an open clearing where he saw someone, he couldn't make out who it was but he could see that it was being chased by three wolves that looked to be made of twigs, logs and leaves.

Without a moment to spare, Link drew his gilled sword, lept over the wolves and got into his fighting stance "back off!" the Hero of Time said in a demanding tone as he pointed his sword in their direction. The wolves didn't seem to be fazed by Links actions as one of them tried lunging at him, unfortunately for them Link was able to dodge the attempted attack and delivered some swift slashes to the attacking creature, causing it to turn to ash mere seconds afterwards.

The other wolves saw to angry look in Links eyes as he repeated his earlier words "I'm giving you on last chance, back off!" the young hylian said causing the wolves the yelp in fear and run off. He then sheathed his sword and started to turn around and ask if the woman he saved was okay "are you alright mi-" Link began only to be tackled to the ground by a brown blur.

"Link! oh sweet merciful Farore, your okay" said a relieved voice that was unfamilliar to the hylian, when Link finally faced what had him pinned down he saw that it was a brown horse with a white mane and a symbol of the Triforce of its flank. But the most shocking aspect of all this was that it just spoke to him and coincidentally it just happened to resembled...

"E-Epona!?" Link exclaimed in shock as the talking horse finally got off him "wh-what happened to you? and how are you able to talk?" the Hero of Time asked still in complete disbelief.

Epona just shrugged at the questions "I honestly don't know, one minute I saw you get pulled into some bright portal thing, but the very next one I'm on my back in this forest and suddenly able to talk, trust me buddy this was a shock to me as well" she said before a look of shock came across her face. "Oh thats right, I found this before I was chased by those wolves" Epona said as she gave Link a familiar blue object.

"My ocarina" Link said as he reached out for the royal families instrument and took it from the brown mare. "Thanks girl, I think Zelda would probthrow me in the castle dungeon if I lost this" Link joked as he sliped the ocarina back into his item pouch, while Epona just gave him a confused look.

"Wow, you sure are taking this 'I can suddenly talk' thing pretty well" the ranch mare said surprised that her friend just accepted this transformation quite quickly.

"Considering on my last quest I was turned into a Deku, a Gorron and a Zora I think that this is pretty minor in comparison" the Hero of Time replied with a small smile before his face became more serious. "But aside from that, I don't think that we're in Hyrule any more" Link said as he scanned the surroundings of the forest.

"What gave it away, the fact that I can suddenly speak now? or was it the wooden wolves that tried to eat me?" Epona said with a deadpaned look on her face before she noticed an nearby exit with a small town in the same direction. "Maybe someone from over there knows where we are?" the ranch mare said pointing her hoof in the direction of the exit.

Link on the other hand was a bit more sceptical "I don't know Epona, something about that place rubs me the wrong way" the cautious former Kokiri said while rubbing his chin curiously.

"I don't like it either Link, but at this moment in time I really don't think we have a choice" said Epona with her voice showing some fear.

"Alright, we'll head over there, but stay close to me in case something happens" Link said earning a nod from his equine friend as the two made their way to the small village outside of the forest.

* * *

This is my first attempt at a MLP/LoZ crossover so the constructive critisicim would help out tremendously. If anyone has any ideas for dungeon puzzles or bosses then post in the comments and i'll see what I can do.


	2. Twilights escape and Ponyvilles ruins

Disclaimer- I own none these properties involved in this crossover

My Little Pony is owned by Hasbro

The Legend of Zelda is owned by Nintendo

Constructive criticism is welcome and encouraged

* * *

Twilight let out a heavy sigh, today was the anniversary of the fall of the Crystal Empire and even though she tried to remain strong for her loved ones she was still depressed over the events that have occurred over the past 10 years. Ever since reclaiming the Crystal Empire, King Sombra had gone on to takeover Equestria starting with Canterlot and Ponyville as well as the enslavement of their citizens.

To top it all off, the dark unicorn had also decided to publicly execute Celestia and Luna to make sure there was no possible way of him being defeated, so needless to say it was getting very difficult for the lavender unicorn to remain positive through all of this. Today was just like every other day for the past couple of years now, she just sat alone in her cell with nothing but her guilty thoughts to keep her company, wondering if things could've gone differently that fateful day.

But today, while the guards where going on their usual rounds two small grenades where rolled into the dungeon, getting the attention of the guards before they exploded creating a huge smoke cloud that impaired Twilights vision. When she looked through the thick smoke, Twilight thought that she could make out the familliar image of an earth pony with her hair tied up and wearing a cowpony hat fighting off the disoriented guards "A-AppleJack?" Twilight said in shock as the earth pony in front of her knocked out the last guard.

"Not exactly Twi' but ah'm still glad to see ya'" came a familiar southern voice that was not exactly AppleJack, but still familiar to Twilight. When the cloud disappeared Twilight saw that the pony through the bars was wearing a black body suit with a brown jacket along with the hat, but the distinctive features of the pony was that she was light yellow and had a red mane and tail.

"Apple Bloom!? what are you doing here?" asked Twilight who was in complete shock at the now fully grown pony.

"What do ya' think sugarcube, gettin' ya outta here" said Apple Bloom as she held the keys to Twilights cell in front of her face. After unlocking the cell door the now teenage crusader motioned for the lavender mare to follow her "sick close ta' me pardner, cause this place is jus' crawlin' with guards" she said as both ponies made a quick escape from the dungeon.

As they made their way out of the dungeon, the two ponies where stopped at the entrance by a group of guards pointing their spears at them. However, before they could react the guards where knocked unconscious by three separate magical blasts of energy "Getting a little slow, wouldn't you say Bloom?" said a joking voice which came from a white unicorn who was wearing the same clothes as Apple Bloom and had a cotton candy styled mane.

"Sorry 'bout that Sweetie Belle, jus' took awhile ta' get past the guards" the former farm fily said to her friend before turning back to Twilight. "Twilight, you remember Sweetie right?" Apple Bloom asked with the lavender unicorn giving a slow nod.

"Well what'd you know, seems like those changelings told the truth after-all" Sweetie Belle with some surprise in her voice.

"Wait a second, what does any of this have to do with changelings?" Twilight asked starting to get confused about the whole situation.

"We'll explain later Twilight, but right now we need to get out of here" said the white unicorn as the three started to make their way through the castles hallways. At least until they where caught at a crossroad by an army of soldiers.

"Shoot, anypony got any bright ideas?" Apple Bloom said with both unicorns shaking there heads in response. The farm pony then got a look at the stained glass window behind her and noticed a small silhouette on the other side, which quickly made up her mind "sorry Twi" she muttered as she bucked the lavender unicorn through the window.

Twilight began falling from the to of the tower they had been in and began plummeting towards the castle's courtyard, screaming in terror in the process. But before she hit the hard concrete bellow her, she was saved by an orange blur which scooped up Twilight and deposited her just outside the Crystal Empires walls.

"Not my personal best time for saving somepony, but you can't argue with results" said a cocky voice that sounded similar to Rainbow Dash, so similar that Twilight didn't even need to look at her rescuer to identify her.

"Let me guess, Scootaloo?" Twilight said who was still trying to find her footing after being kicked out of the tower. Sure enough, when Twilight got a look at her it was indeed an orange pegasus with a purple mane, unlike Apple Bloom and Sweetie Belle however, Scootaloo had her crusader cape tied around her right eye like an eye patch, which made it obvious she'd been in some large conflict of some sorts.

"The one and only" Scootaloo said to the stunned unicorn "but seriously, its good to see you again Twilight and might I add you look good for someone who's been locked up for this long" the pegasus said with some obvious cockiness in her voice as Sweetie Belle and Apple Bloom appeared behind them in a bright flash of light.

"Sorry 'bout kickin' ya' through the window Twilight" apologised the yellow earth pony to the lavender unicorn. "Ah was jus' put on the spot and wasn't thinkin' straight" Apple Bloom continued before Twilight just gave the Cutie Mark Crusaders a small smile.

"It's okay girls I understand" Twilight said as the three ponies in front of her just ran up and gave Twilight a big group hug. "Theres just one thing I want to know, what are the three of you doing here?" the lavender mare asked with some curiosity in her voice.

"Isn't it obvious, we came to save you from King Sombra, thats what" Sweetie Belle replied in the same way she would usually answer a question, so at least that stayed the same from her filyhood.

Twilight simply rolled her eyes and face-hoofed in response "I know that already Sweetie, what I mean is why now of all times?" Celestia's former student said now asking the CMC in a more serious tone of voice.

The Crusaders looked a little bit unsure on how to answer this until Scootaloo spoke up "To be perfectly honest with you Twilight, we thought Sombra had turned you to his side like the others, or worse" the pegasus said in a depressed tone and earning a look of shock from the others. "We only found out you where in the dungeon because of the changeling spies that we sent out just last week, sorry about the long wait" Scootaloo finished in a sad tone.

Twilight on the other had just had a look of confusion and shock on her face "changeling spies?" she said in an uncertain tone.

"We'll explain later Twilight, but right now lets get you back to HQ" Apple Bloom said in an informative tone as the three crusaders led Twilight towards the Everfree Forest. "Sides' we have a lot of catchin' up ta' do" the earth pony said as they disappeared into the dark forest.

* * *

"Welcome to Ponyville, population: ponies" Epona read from a broken sign as both she and Link stood outside the small village. "Wow, and I thought Kakariko was an odd name for a village" the ranch mare said with a confused look on her face.

"Just try to stay close girl, this place doesn't look very friendly" Link said as he and his horse walked through the almost abandoned village. "Hello! is anybody here!?" the Hero of Time called out hoping to get the attention of some citizens, to his disappointment however there was no sign of anyone in the whole village.

"This place looks kinda like a ghost town Link, I'm starting to regret coming here in the first place" said Epona who was now starting to show some fear in the way she spoke.

Link was about to say that she shouldn't worry about anything, but in actuallity the Hero of Time was feeling the same way and it didn't help that the atmosphere and the way the town looked reminded him of Castle Town when Ganondorf took over Hyrule. Eventually, the duo came across a half destroyed tree which also looked like it had previously been a house and outside the tree house was a golden sign which read 'Golden Oak Library.'

Being the curious type, Link began to walk towards the empty husk of the tree despite the protests from Epona not to do so. "I'll be fine Epona, just wait out here until I get back" reassured Link as he entered the abanndoned library.

The whole place looked like it had been ransacked as the bookcase's had been overturned and many of them where missing their contents "What happened to this place?" Link questioned to himself as he continued to search through the empty building. As he was searching, the Hero of Time came across a broken picture frame with a picture of a bunch of multi-coloured horses inside it.

"Hang on a second" said Link as he decided to take a closer look at the photo and noticed the marks on their flanks. "Those are the same markings from the cave, but what does this have to do with that?" the Hero of Time said in a curious voice as he eyed the photo with a eyebrow raised.

But his curious nature didn't last long as he heard Epona outside, who sounded like she was in trouble. "Hey! lemme go!" her voice called out in a struggling tone, almost instantly Link ran out of the tree and saw Epona being held by two other horses wearing black armour.

"This area is off limits to ponies like you, now stop struggling or you'll be suspected of aiding the resistance" one of the horses said as Epona continued to struggle to get out of their grasp. Noticing the trouble his friend was in Link charged at the two armoured horses while taking out his hookshot.

"YOU LEAVE HER ALONE!" Link shouted as he fired the spring loaded chain at one of the horses, causing it to lose its grip on Epona. As the other horse saw this so it pulled out a spear and tried to rush the young hylian, who was able to counter by pulling out his sword and performing three swift strikes which caught the horse he was fighting off guard.

The fight wasn't very long because as soon as the horse lunged at him with the spear for a second time, Link just side-steped around him and whacked it on the back of his head with the hilt of his sword, knocking it unconscious in the process. However, as soon Link sheathed his sword the horse that he used his hookshot on earlier recovered and bucked Link clean in the chest, pinning him to the ground before he could recover.

The horse then pulled out a small dagger and was about to drive it through Link's chest, that is until Epona tackled the armoured creature and just started to wail on it. "Get away from him!" the ranch mare said as she delivered a quick kick to the horse's face, knocking this one out as well.

Epona then turned to Link to help him up "you okay buddy?" she asked as offered the hylian a hoof up.

"Yeah, thanks for the help" the ex-Kokiri said as Epona pulled him up to his feet, the two of them examined their attackers. "So, I think its safe to assume that this world is inhabited by talking horses" the Hero of Time said to his companion who nodded in response.

However before Epona could say anything the duo was suddenly surrounded by a whole squad of soldiers. "By the order of King Sombra, the two of you are under arrest for trespassing on a restricted area and assault on the obsidian guard" the captain said as the horses started to advance on the two of them.

Without a second thought, Link grabbed Epona by her hoof and pulled out a clear crystal with a green gem in the middle of it from his item pouch. "FARORE'S WIND!" Link exclaimed as the crystal began glowing brightly and engulfing the hylian duo at the same time, when the light finally subsided Link and Epona where nowhere to be seen.


End file.
